Filling the gap - COI barcode resolution in eastern Palearctic birds

Abstract

BackgroundThe Palearctic region supports relatively few avian species, yet recent molecular studies have revealed that cryptic lineages likely still persist unrecognized. A broad survey of cytochrome c oxidase I (COI) sequences, or DNA barcodes, can aid on this front by providing molecular diagnostics for species assignment. Barcodes have already been extensively surveyed in the Nearctic, which provides an interesting comparison to this region; faunal interchange between these regions has been very dynamic. We explored COI sequence divergence within and between species of Palearctic birds, including samples from Russia, Kazakhstan, and Mongolia. As of yet, there is no consensus on the best method to analyze barcode data. We used this opportunity to compare and contrast three different methods routinely employed in barcoding studies: clustering-based, distance-based, and character-based methods.ResultsWe produced COI sequences from 1,674 specimens representing 398 Palearctic species. These were merged with published COI sequences from North American congeners, creating a final dataset of 2,523 sequences for 599 species. Ninety-six percent of the species analyzed could be accurately identified using one or a combination of the methods employed. Most species could be rapidly assigned using the cluster-based or distance-based approach alone. For a few select groups of species, the character-based method offered an additional level of resolution. Of the five groups of indistinguishable species, most were pairs, save for a larger group comprising the herring gull complex. Up to 44 species exhibited deep intraspecific divergences, many of which corresponded to previously described phylogeographic patterns and endemism hotspots.ConclusionCOI sequence divergence within eastern Palearctic birds is largely consistent with that observed in birds from other temperate regions. Sequence variation is primarily congruent with taxonomic boundaries; deviations from this trend reveal overlooked biological patterns, and in some cases, overlooked species. More research is needed to further refine the taxonomic status of some Palearctic birds, but large genetic surveys such as this may facilitate this effort. DNA barcodes are a practical means for rapid species assignment, although efficient analytical methods will likely require a two-tiered approach to differentiate closely related pairs of species.

DNA barcoding and evolutionary relationships of the Phasianidae family in China

“…Previous studies have successfully used the COI gene to discriminate bird species (Kerr et al, 2009;Johnsen et al, 2010;Ong et al, 2011;Arif et al, 2011;Breman et al, 2013). Recent reports have also extended the application of COI gene analysis into phylogenetic research (Arif et al, 2011;Breman et al, 2013).…”

“…Large-scale standardized sequencing of COI has made DNA barcoding an efficient species identification tool for many animal groups (Hebert et al, 2003). Previous barcoding studies of birds have mainly focused on the survey of regional groups, in areas such as Korea (Yoo et al, 2006;Park et al, 2011), North America (Kerr et al, 2007), Southeast Asia (Lohman et al, 2009), the Neotropics (Vilaca et al, 2006;Kerr et al, 2009), and Scandinavia (Johnsen et al, 2010). However, DNA barcoding studies on specific taxa, such as Galliformes birds, remain limited.…”

<b>Genetic and taxonomic relationships of five species of Rallidae (Aves: Gruiformes) based on mitochondrial cytochrome oxidase subunit I sequences

“…Until now, performance of the COI region for genetic identification and classification have been evaluated in many birds (Yoo et al, 2006;Kerr et al, 2007;Chaves et al, 2008;Kerr et al, 2009a;Kerr et al, 2009b). The present study based on COI gene sequencing data of three genera and five species of the family Rallidae revealed different systematic classification of the current classification and question existence of genus Gallinula.…”

Genetic Divergence of the Species of the Yellow Wagtails Group (Passeriformes, Motacillidae) in European Territory of Russia

“…Cytochrome C oxidase I gene site was amplifi ed using forward primer -ttctccaaccacaaagacattggcac and reverse primer -acgtgggagataattccaaatcctgg (Kerr et al, 2009). Quality of the PCR product was detected with analytical gel-electrophoresis.…”

“…In spite of the wide sympatry in nesting area there is selective mating between males and females of each of the studied species which inhibits free crossing and supports insulating mechanisms in populations. (Zarudny, 1891;Beregovoy, 1970;Babenko, 1981;Bakhtadze, 1987;Grichik, 1992;Red'kin, а, 2001Sotnikov, 2006;Artemieva, Muraviev, 2012 а;Pavlova et al, 2003;Kerr et al, 2009).…”